Abstract

Background

Seed plants are composed of angiosperms and gymnosperms, which diverged from each
other around 300 million years ago. While much light has been shed on the mechanisms
and rate of genome evolution in flowering plants, such knowledge remains conspicuously
meagre for the gymnosperms. Conifers are key representatives of gymnosperms and the
sheer size of their genomes represents a significant challenge for characterization,
sequencing and assembling.

Results

To gain insight into the macro-organisation and long-term evolution of the conifer
genome, we developed a genetic map involving 1,801 spruce genes. We designed a statistical
approach based on kernel density estimation to analyse gene density and identified
seven gene-rich isochors. Groups of co-localizing genes were also found that were
transcriptionally co-regulated, indicative of functional clusters. Phylogenetic analyses
of 157 gene families for which at least two duplicates were mapped on the spruce genome
indicated that ancient gene duplicates shared by angiosperms and gymnosperms outnumbered
conifer-specific duplicates by a ratio of eight to one. Ancient duplicates were much
more translocated within and among spruce chromosomes than conifer-specific duplicates,
which were mostly organised in tandem arrays. Both high synteny and collinearity were
also observed between the genomes of spruce and pine, two conifers that diverged more
than 100 million years ago.

Conclusions

Taken together, these results indicate that much genomic evolution has occurred in
the seed plant lineage before the split between gymnosperms and angiosperms, and that
the pace of evolution of the genome macro-structure has been much slower in the gymnosperm
lineage leading to extent conifers than that seen for the same period of time in flowering
plants. This trend is largely congruent with the contrasted rates of diversification
and morphological evolution observed between these two groups of seed plants.